I would like to use a site found by SiteMap as input to Glide docking. How do I do this ?

You can use a SiteMap site to generate a Glide grid as follows:

1. Display the protein and the site of interest from SiteMap by including them in the Maestro Workspace.
2. Choose Applications → Glide → Receptor Grid Generation.
3. In the Receptor tab, choose Molecule from the Pick to identify ligand option menu.
4. Carefully select the site point where you want the center of the Glide grid box to be. If you select the incorrect point, just pick again until the correct one is hightlighted with a blue square.
5. Click the Site tab. The purple enclosing box is displayed, but it is too small.
6. Under Center, click "Supplied X,Y,Z coordinates".
7. Under Size, select "Dock ligands with length", and adjust the slider to your desired value.

IMPORTANT: Now that the enclosing box has been defined, it is necessary to exclude the site entry from the Workspace, or it will be incorrectly included in the receptor.


8. Control-click the site entry in the Project Table to exclude the site entry. The site points are no longer in the Workspace, but the grid box should remain.
9. Fill in any additional options in the Grid Generation panel, and click Start.

Keywords: SiteMap, Glide, docking, site points

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